SMTL ID : 2g64.1

Structure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

12 x NA: SODIUM ION(Non-functional Binders)

NA.1: 7 residues within 4Å: Chain A: N.47, V.49, E.128, E.129, T.130, P.131 Chain E: N.47 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.130, E:N.47 NA.2: 7 residues within 4Å: Chain A: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.40, A:G.43 NA.5: 7 residues within 4Å: Chain B: N.47, V.49, E.128, E.129, T.130, P.131 Chain D: N.47 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.128, D:N.47 NA.6: 7 residues within 4Å: Chain B: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.19, B:G.43 NA.9: 7 residues within 4Å: Chain C: N.47, V.49, E.128, E.129, T.130, P.131 Chain F: N.47 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.47, C:T.130 NA.10: 7 residues within 4Å: Chain C: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.40, C:G.43 NA.13: 7 residues within 4Å: Chain B: N.47 Chain D: N.47, V.49, E.128, E.129, T.130, P.131 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.47, D:E.129 NA.14: 7 residues within 4Å: Chain D: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.40, D:G.43 NA.17: 7 residues within 4Å: Chain A: N.47 Chain E: N.47, V.49, E.128, E.129, T.130, P.131 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.47, E:E.129 NA.18: 7 residues within 4Å: Chain E: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.40, E:G.43 NA.21: 7 residues within 4Å: Chain C: N.47 Chain F: N.47, V.49, E.128, E.129, T.130, P.131 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:T.130, C:N.47 NA.22: 7 residues within 4Å: Chain F: H.19, R.20, C.38, N.39, N.40, G.43, H.44 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.19, F:G.43

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.19, A:H.44, A:H.46, H2O.6, H2O.29 ZN.7: 3 residues within 4Å: Chain B: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.19, B:H.44, B:H.46, H2O.12, H2O.23 ZN.11: 3 residues within 4Å: Chain C: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.19, C:H.44, C:H.46, H2O.19, H2O.36 ZN.15: 3 residues within 4Å: Chain D: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.19, D:H.44, D:H.46, H2O.10, H2O.25 ZN.19: 3 residues within 4Å: Chain E: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.19, E:H.44, E:H.46, H2O.4, H2O.31 ZN.23: 3 residues within 4Å: Chain F: H.19, H.44, H.46 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.19, F:H.44, F:H.46, H2O.17, H2O.38

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.53, Y.123, K.124, K.138 Ligands: GOL.8, GOL.12 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.53, A:K.53, A:Y.123, A:K.124, A:K.138 Water bridges: B:K.53 GOL.8: 6 residues within 4Å: Chain B: K.53, Y.123, K.124, K.138 Ligands: GOL.4, GOL.12 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.53, B:K.53, B:Y.123, B:K.124, B:K.138 Water bridges: C:K.53 GOL.12: 6 residues within 4Å: Chain C: K.53, Y.123, K.124, K.138 Ligands: GOL.4, GOL.8 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.53, C:K.53, C:Y.123, C:K.124, C:K.138 Water bridges: A:K.53 GOL.16: 6 residues within 4Å: Chain D: K.53, Y.123, K.124, K.138 Ligands: GOL.20, GOL.24 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.53, D:K.53, D:Y.123, D:Y.123, D:K.124, D:K.138 Water bridges: E:K.53 GOL.20: 6 residues within 4Å: Chain E: K.53, Y.123, K.124, K.138 Ligands: GOL.16, GOL.24 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.53, E:K.53, E:Y.123, E:Y.123, E:K.124, E:K.138 Water bridges: F:K.53 GOL.24: 6 residues within 4Å: Chain F: K.53, Y.123, K.124, K.138 Ligands: GOL.16, GOL.20 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain F Water bridges: D:K.53 Hydrogen bonds: F:K.53, F:K.53, F:Y.123, F:Y.123, F:K.124, F:K.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wengerter, B.C. et al., Crystal Structure of Caenorhabditis Elegans 6-Pyruvoyl Tetrahydropterin Synthase. To be Published

Release Date

2006-03-14

Peptides

Putative 6-pyruvoyl tetrahydrobiopterin synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Putative 6-pyruvoyl tetrahydrobiopterin synthase